key: cord-0730702-9vrlgxxq
authors: Oliveira, Gabriella S.; Silva‐Flannery, Luciana; Silva, Juliana F.; Siza, Charlene; Esteves, Roberto J.; Marston, Barbara J.; Morgan, Juliette; Plucinski, Mateusz; Roca, Tárcio P.; Silva, Ana M. P.; Pereira, Soraya S.; Salcedo, Juan M. V.; Pereira, Dhelio B.; Naveca, Felipe G.; Vieira Dall'Acqua, Deusilene S.
title: Active surveillance and early detection of community transmission of SARS‐CoV‐2 Mu variant (B.1.621) in the Brazilian Amazon
date: 2022-03-22
journal: J Med Virol
DOI: 10.1002/jmv.27686
sha: 7d6e8916c12c7bde6a1f264867bf518650e347f4
doc_id: 730702
cord_uid: 9vrlgxxq

Through active surveillance and contact tracing from outpatients, we aimed to identify and characterize SARS‐CoV‐2 variants circulating in Porto Velho‐Rondônia, a city in the Brazilian Amazon. As part of a prospective cohort, we gathered information from 2,506 individuals among COVID‐19 patients and household contacts. Epidemiological data, nasopharyngeal swabs, and blood samples were collected from all participants. Nasopharyngeal swabs were tested for antigen rapid diagnostic test and reverse transcription‐polymerase chain reaction (RT‐PCR) followed by genomic sequencing. Blood samples underwent ELISA testing for IgA, IgG, and IgM antibody levels. From 757 specimens sequenced, three were identified as Mu variant, none of the individuals carrying this variant had a travel history in the previous 15 days before diagnosis. One case was asymptomatic and two presented mild symptoms. Two infected individuals from different households caring viruses with additional amino acid substitutions ORF7a P45L and ORF1a T1055A compared to the Mu virus reference sequence. One patient presented IgG levels. Our results highlight that genomic surveillance for SARS‐CoV‐2 variants can assist in detecting the emergency of SARS‐CoV‐2 variants in the community, before its identification in other parts of the country.

Monitoring detection of SARS-CoV-2 variants of interest (VOI) across geographic regions provides information on VOIs spread and may aid early identification and characterization of variants of concern (VOC). antibody responses and increased transmissibility. [2] [3] [4] Many of those mutations (T95I, E484K, N501Y, D614G, P681H, and D950) are also present in Gamma and Delta VOCs. 5 Although the majority of the cases have been reported in South America and the Caribbean, the Mu variant has also been identified in North America, Europe, and Asia. 6 Brazil has the highest number of reported cases of coronavirus disease 2019 in South America since the beginning of the pandemic (followed by Argentina We also visited the household to collect further epidemiological data, nasal and nasopharyngeal swabs, and blood specimens from all individuals. We followed index case-patients and household contacts for 14 days. All nasopharyngeal specimens underwent reverse transcription-polymerase chain reaction (RT-PCR) using Allplex 2019-nCoV assay (Seegene) 9 Table 1 ).

Serologic testing of blood specimens collected June 18 tested negative by SARS-CoV-2 antigen-specific IgM, IgA, and IgG assays.

This patient remained RT-PCR positive on follow-up testing on July 1 with a C t of 24, estimated viral load of 10 6.18 copies/mL.

A nasopharyngeal specimen collected June 18, 2021, from the mother of Case 2 tested positive by SARS-CoV-2 RT-qPCR with C t of 27 and an estimated viral load of 10 5.2 copies/mL. The patient was a 58-year-old, healthy female with no underlying medical conditions who complained of cough with onset 2 days prior but had no other symptoms and tested 

The authors thank the Laboratório Central de Saúde Pública de Rondônia (LACEN) for the initial sample processing, and the support provided by the Fiocruz COVID-19 Genomic Surveillance Network

) and the Respiratory Viruses Genomic Surveillance Network of the Brazilian Ministry of Health Central Laboratory Coordination (Coordenação Geral de Laboratórios de Saúde Pública CGLAB). The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for

Laboratório de Virologia Molecular, Fundação Oswaldo Cruz, Fiocruz, Rondônia, Brazil) and Fernanda C. Lessa (Centers for Diseases Control and Prevention (CDC)

Writing-original draft: Gabriella S

Writing -review

Funding acquisition: Juliette Morgan

All authors approved the final version

Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

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Boletim Epidemiológico Especial 100-Doença pelo Coronavírus COVID-19/Ministério da Saúde e Secretaria de Vigilância em Saúde

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The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?

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COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

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Correlation between a quantitative anti-SARS-CoV-2 IgG ELISA and neutralization activity

Active surveillance and early detection of community transmission of SARS-CoV-2 Mu variant (B.1.621) in the Brazilian Amazon

All SARS-CoV-2 genomes generated and analyzed in this study are available at the EpiCoV database in GISAID (https://www.gisaid.org) with accession IDs EPI_ISL_10115640, EPI_ISL_10115641, and EPI_ISL_10115642.

Luciana Silva-Flannery https://orcid.org/0000-0002-5762-8451